LaTeX math (and even macros) can be used in markdown documents. Several different methods of rendering math in HTML are provided, including MathJax and translation to MathML. LaTeX math is rendered in docx using native Word equation objects.

Pandoc includes a powerful system for automatic citations and bibliographies, using pandoc-citeproc (which derives from Andrea Rossato’s citeproc-hs). This means that you can write a citation like

[see @doe99, pp. 33-35; also @smith04, ch. 1]

and pandoc will convert it into a properly formatted citation using any of hundreds of CSL styles (including footnote styles, numerical styles, and author-date styles), and add a properly formatted bibliography at the end of the document. Many forms of bibliography database can be used, including bibtex, RIS, EndNote, ISI, MEDLINE, MODS, and JSON citeproc. Citations work in every output format.

Pandoc includes a Haskell library and a standalone command-line program. The library includes separate modules for each input and output format, so adding a new input or output format just requires adding a new module.